Question 1: true they will not show in restore of course.
Question 2: backup files (.mbz) that were stored in moodledata/filedir/ will remain as long as they show in the course restore menu. If a teacher made a backup of a course, those were stored in the teachers private files area. An admin user cannot see those via course restore as admin, login as teacher to see them/edit them (cli removal is more efficient - more on that further down).
Question 3: would assume so ... but then again ... no one here is really familiar with your setup!
Question about backup file 're-registration' .... am gonna say no ... and why would anyone want to (that's food for thought)?
Manual removal of a .mbz file is a 2-3 step process involving a DB query of mdl_files to find the contenthash value, locating that contenthash value filename in /moodledata/xx/yy/xxyybunchoflettersnumbers file, manually removing that file, then going back to mdl_files table and removing that row.
When automated backups goes south, one might need to truncate tables related in DB to get a clean slate.
The important thing, of course, especially if this is an all-in-one server ... DB and moodledata physically on same server ... never run out of space as that could lead to corruption of the DB for the site. 90% would make me very uncomfortable as one Teacher making multiple backups of their course on their own could possibly use up space.
Consider installing moosh as it does have some commands that might prove useful to you.
'SoS', Ken